Sequence data handling by computer.

The speed of the new DNA sequencing techniques has created a need for computer programs to handle the data produced. This paper describes simple programs designed specifically for use by people with little or no computer experience. The programs are for use on small computers and provide facilities for storage, editing and analysis of both DNA and amino acid sequences. A magnetic tape containing these programs is available on request.     

EMBOSS软件包序列分析程序应用实例

本文介绍欧洲分子生物学开放软件包EMBOSS序列分析程序应用实例.第1节简单介绍EMBOSS软件包的概况和基本用法.第2节介绍格式转换、序列提取、序列变换和序列显示等常用序列处理程序.第3节介绍序列比对程序,包括双序列比对、多序列比对和点阵图程序.第4节介绍常用核酸序列分析程序,可用于核苷酸组分统计、开放读码框分析、C...     

EQA from an Australian perspective

Enrolment in external quality assurance programs is part of the accreditation process for medical laboratories in Australia, with the majority of Australian laboratories being enrolled in programs from RCPA Quality Assurance Programs Pty Limited, a company owned by the Royal College of Pathologists of Australasia. An important feature of these programs is that they have been developed with the involvement and contribution of the profession. For example, the Chemical Pathology programs are a joint venture between the company and the Australasian Association of Clinical Biochemists (AACB). Some of the unique features of the programs are the composition of the material, the use of target values, the structure and information in the reports and the use of the internet for data entry and data review. Over the past thirty years, the development of these programs has made a significant contribution to the quality of laboratories in Australia.     

Components and Characteristics of Youth Development Programs: The Voices of Youth-Serving Policymakers,Practitioners, Researchers,and Adolescents

Due to its increasing popularity, youth development (YD) has become a buzzword that is attached to a variety of programs. Several attempts have been made to articulate a unified definition of YD that would enable the field to progress toward measuring the effectiveness of YD programs. In order to determine what constitutes a YD program, we must establish the criteria for inclusion. This is an exploratory study of a collaborative approach to understanding the components and characteristics of YD programs. The objective of this study is to compare and contrast responses across four participant groups (policymakers, practitioners, researchers, and youth) using a community-based participatory approach, in order to reach consensus and explore the perceived hierarchy of key characteristics for YD programs from multiple stakeholder perspectives.     

中国种子植物区系定量化研究 Ⅱ.多地区种子植物区系研究实用程序工作原理(DDBJ-系列程序)

本文介绍了定量化研究多个种子植物区系的电子计算机程序（DDAI）工作原理,简要讨论以共有属构建的区系间相似关系问题。应用本文提出的程序,可一次性完成所有被研究区系种子植物分布区类型的统计及有关的计算工作,同时也可根据各分布区类型及总体共有属,构建各个区系间的相似性系数及其他有关的参数。本文以中国若干种子植物区系原始资料统计计算为例提供的CAR（Computer Aided Research）方法,可对全面深入地研究中国种子植物区系,提供强有力的工具。     

Population programs for the detection of couples at risk for severe monogenic genetic diseases

Population genetic screening programs for carrier detection of severe genetic disorders exist worldwide, mainly for beta-thalassemia. These screening programs are either mandatory or voluntary. In several Arab countries and Iran, the state has made thalassemia carrier detection mandatory, while tests for detecting carriers are required by the religious authorities in Cyprus. In all the existing mandatory genetic screening programs, the couples have to get the information about the tests before marriage, but the decision whether or not to marry is left to them. Voluntary programs exist for instance in several Mediterranean countries for the prevention of thalassemia and for several genetic diseases among Jews. While voluntary programs leave the decision to be screened or not to the individual, a major problem is that in many cases awareness about the existence of screening tests is very sparse. Some programs, for instance in Canada or Australia, therefore provide education about genetic tests and screening at school in order to allow the individuals to be able to make an informed decision about their reproductive choices. This article represents the opinions of the author and not necessarily those of the Ministry.     

Environmental enrichment for laboratory rodents: animal welfare and the methods of science

Because of the difficulty of' establishing objective measures of laboratory rodents' psychological well-being, developing environmental enrichment programs that are actually beneficial to rodents destined to participate in laboratory research is particularly challenging. Many studies of effects of environmental complexity, social housing, and increases in cage size suggest that professional judgments as to the impact of diverse types of environmental enrichment on rodent welfare are not a reliable basis for evaluating the outcomes of enrichment programs for laboratory rodents. Successful enrichment programs will vary from one rodent species to another, between sexes, as well as between age classes. There is a need for objective, measurable goals for proposed environmental enrichment programs for rodents, as well a s for empirical investigations of the beneficial and detrimental consequences of proposed environmental manipulations.     

Evaluation of Gene Structure Prediction Programs

We evaluate a number of computer programs designed to predict the structure of protein coding genes in genomic DNA sequences. Computational gene identification is set to play an increasingly important role in the development of the genome projects, as emphasis turns from mapping to large-scale sequencing. The evaluation presented here serves both to assess the current status of the problem and to identify the most promising approaches to ensure further progress. The programs analyzed were uniformly tested on a large set of vertebrate sequences with simple gene structure, and several measures of predictive accuracy were computed at the nucleotide, exon, and protein product levels. The results indicated that the predictive accuracy of the programs analyzed was lower than originally found. The accuracy was even lower when considering only those sequences that had recently been entered and that did not show any similarity to previously entered sequences. This indicates that the programs are overly dependent on the particularities of the examples they learn from. For most of the programs, accuracy in this test set ranged from 0.60 to 0.70 as measured by the Correlation Coefficient (where 1.0 corresponds to a perfect prediction and 0.0 is the value expected for a random prediction), and the average percentage of exons exactly identified was less than 50%. Only those programs including protein sequence database searches showed substantially greater accuracy. The accuracy of the programs was severely affected by relatively high rates of sequence errors. Since the set on which the programs were tested included only relatively short sequences with simple gene structure, the accuracy of the programs is likely to be even lower when used for large uncharacterized genomic sequences with complex structure. While in such cases, programs currently available may still be of great use in pinpointing the regions likely to contain exons, they are far from being powerful enough to elucidate its genomic structure completely.     

Addressing consumer grievances in medicine: policies and practices of newborn screening programs in the United States

Newborn screening programs collectively administer the largest genetic testing initiative in the United States. The redress of grievances is an important mechanism for consumers to provide input into clinical and public health programs. In this study, we evaluated mechanisms for addressing consumer grievances in newborn screening programs. To do this, we surveyed all 50 state plus the District of Columbia newborn screening programs by questionnaire regarding protocols for receipt and redress of problems reported by parents of newborns and ascertained the existence and nature of complaints and how complaints were documented and addressed. Pertinent state and federal legislation and regulation were also reviewed. Six of 49 newborn screening programs reported having formal policies for handling consumer grievances. Four states reported having pertinent legislation or regulation. Thirty-eight of 49 states reported having received complaints from 1993 to 1995. Thirteen of 49 newborn screening programs reported that they actively seek feedback from consumers. Consumer grievances ranged from minor complaints to potentially life-threatening concerns. In general, complaints are managed on an ad hoc basis; formal policies are typically lacking. As newborn screening programs affect a vast number of Americans, a proactive and comprehensive approach, including solicitation of consumer feedback, could benefit both newborn screening programs and the public served by them.     

Environmental Enrichment for Laboratory Rodents: Animal Welfare and the Methods of Science

Because of the difficulty of' establishing objective measures of laboratory rodents' psychological well-being, developing environmental enrichment programs that are actually beneficial to rodents destined to participate in laboratory research is particularly challenging. Many studies of effects of environmental complexity, social housing, and increases in cage size suggest that professional judgments as to the impact of diverse types of environmental enrichment on rodent welfare are not a reliable basis for evaluating the outcomes of enrichment programs for laboratory rodents. Successful enrichment programs will vary from one rodent species to another, between sexes, as well as between age classes. There is a need for objective, measurable goals for proposed environmental enrichment programs for rodents, as well a s for empirical investigations of the beneficial and detrimental consequences of proposed environmental manipulations.     

Monitoring programs of the U.S. Gulf of Mexico: inventory,development and use of a large monitoring database to map fish and invertebrate spatial distributions

Since the onset of fisheries science, monitoring programs have been implemented to support stock assessments and fisheries management. Here, we take inventory of the monitoring programs of the U.S. Gulf of Mexico (GOM) surveying fish and invertebrates and conduct a gap analysis of these programs. We also compile a large monitoring database encompassing much of the monitoring data collected in the U.S. GOM using random sampling schemes and employ this database to fit statistical models to then map the spatial distributions of 61 fish and invertebrate functional groups, species and life stages of the U.S. GOM. Finally, we provide recommendations for improving current monitoring programs and designing new programs, and guidance for more comprehensive use and sharing of monitoring data, with the ultimate goal of enhancing the inputs provided to stock assessments and ecosystem-based fisheries management (EBFM) projects in the U.S. GOM. Our inventory revealed that 73 fisheries-independent and fisheries-dependent programs have been conducted in the U.S. GOM, most of which (85%) are still active. One distinctive feature of monitoring programs of the U.S. GOM is that they include many fisheries-independent surveys conducted almost year-round, contrasting with most other marine regions. A major sampling recommendation is the development of a coordinated strategy for collecting diet information by existing U.S. GOM monitoring programs for advancing EBFM.     

Accessible high-throughput virtual screening molecular docking software for students and educators

We survey low cost high-throughput virtual screening (HTVS) computer programs for instructors who wish to demonstrate molecular docking in their courses. Since HTVS programs are a useful adjunct to the time consuming and expensive wet bench experiments necessary to discover new drug therapies, the topic of molecular docking is core to the instruction of biochemistry and molecular biology. The availability of HTVS programs coupled with decreasing costs and advances in computer hardware have made computational approaches to drug discovery possible at institutional and non-profit budgets. This paper focuses on HTVS programs with graphical user interfaces (GUIs) that use either DOCK or AutoDock for the prediction of DockoMatic, PyRx, DockingServer, and MOLA since their utility has been proven by the research community, they are free or affordable, and the programs operate on a range of computer platforms.     

Apple II software for M13 shotgun DNA sequencing.

A set of programs is presented for the reconstruction of a DNA sequence from data generated by the M13 shotgun sequencing technique. Once the sequence has been established and stored other programs are used for its analysis. The programs have been written for the Apple II microcomputer. A minimum investment is required for the hardware and the software is easily interchangeable between the growing number of interested researchers. Copies are available in ready to use form.     

Screening protein and nucleic acid sequences against libraries of patterns.

We describe programs that can screen nucleic acid and protein sequences against libraries of motifs and patterns. Such comparisons are likely to play an important role in interpreting the function of sequences determined during large scale sequencing projects. In addition we report programs for converting the Prosite protein motif library into a form that is compatible with our searching programs. The programs work on VAX and SUN computers.     

Trends and values of ‘Land for Wildlife’ programs for private land conservation

The Land for Wildlife program started in Victoria in 1981 as a voluntary program with the broad aim of supporting landholders in providing habitat for wildlife on their property. The program has since spread across Australia and is implemented in a range of guises, through a variety of governance approaches. This research collected qualitative and quantitative data on Land for Wildlife programs across Australia to conduct the first national review. Data were gathered on changes in program membership to assess different participation trends. In addition, phone interviews with Land for Wildlife coordinators throughout Australia were conducted to explore how the programs are positioned in delivering biodiversity outcomes in a range of different regions. Over 14,000 properties covering 2.3 million ha are currently registered under Land for Wildlife programs. with at least 500,000 ha of habitat managed for conservation. Limited resources present a large challenge faced by a number of programs, with generally low funding and staffing resulting in restricted biodiversity focus and conservation outcomes. We suggest options to enhance the programs and propose future research directions.     

Opportunity gaps in out-of-school learning: How structural and process features of programs relate to race and socioeconomic status

Abstract

Out-of-school learning programs can be a context for positive development and learning for children and youth. However, research points to potential racial and socioeconomic disparities, or opportunity gaps, in this context. In this study, we use survey and video data from 106 staff across 30 out-of-school programs to examine how three features, staff, activities, and adult–child interactions, differ based on the racial and socioeconomic makeup of programs. We find that staff at programs serving children from low-income families on average have less experience and education. Also, programs serving children from African American and low-income families tend to offer more academic-focused activities. Finally, we found no differences in adult–child interaction quality across programs in the sample. Our findings suggest that a racial and socioeconomic opportunity gap may exist in the out-of-school context. This has implications for educational equity and the positive development of children that participate in this context.     

The current status and portability of our sequence handling software.

I describe the current status of our sequence analysis software. The package contains a comprehensive suite of programs for managing large shotgun sequencing projects, a program containing 61 functions for analysing single sequences and a program for comparing pairs of sequences for similarity. The programs that have been described before have been improved by the addition of new functions and by being made very much easier to use. The major interactive programs have 125 pages of online help available from within them. Several new programs are described including screen editing of aligned gel readings for shotgun sequencing projects; a method to highlight errors in aligned gel readings, new methods for searching for putative signals in sequences. We use the programs on a VAX computer but the whole package has been rewritten to make it easy to transport it to other machines. I believe the programs will now run on any machine with a FORTRAN77 compiler and sufficient memory. We are currently putting the programs onto an IBM PC XT/AT and another micro running under UNIX.